Mercurial > repos > iuc > stacks2_denovomap
diff stacks_denovomap.xml @ 1:afdbc7fcce70 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
| author | iuc |
|---|---|
| date | Mon, 30 Sep 2019 14:17:15 -0400 |
| parents | b9822370f843 |
| children | 421c33b8bf17 |
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--- a/stacks_denovomap.xml Mon Jul 01 11:04:37 2019 -0400 +++ b/stacks_denovomap.xml Mon Sep 30 14:17:15 2019 -0400 @@ -7,7 +7,11 @@ <expand macro="version_cmd"/> <command detect_errors="aggressive"><![CDATA[ @FASTQ_INPUT_FUNCTIONS@ -mkdir stacks_inputs stacks_outputs&& +mkdir stacks_inputs stacks_outputs && + +#if $output_log + ln -s '$output_log' stacks_outputs/denovo_map.log && +#end if #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, ".%d" ) $link_command @@ -35,7 +39,6 @@ ## to make it usable in Galaxy (with the downside that we ## need to gzip it again for downstream calls like populations) && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf -&& mv stacks_outputs/denovo_map.log $output_log ]]></command> <inputs> @@ -161,11 +164,11 @@ <assert_command> <has_text text="-M 3" /> <has_text text="-n 3" /> - <has_text text="\-\-var-alpha 0.1" /> - <has_text text="\-\-gt-alpha 0.1" /> - <has_text text="\-\-rm-pcr-duplicates" /> - <has_text text="\-\-min-samples-per-pop 1" /> - <has_text text="\-\-min-populations 0" /> + <has_text text="--var-alpha 0.1" /> + <has_text text="--gt-alpha 0.1" /> + <has_text text="--rm-pcr-duplicates" /> + <has_text text="--min-samples-per-pop 1" /> + <has_text text="--min-populations 0" /> </assert_command> <output_collection name="tabs" count="6"/> <output_collection name="catalog" type="list" count="3"/>